Basic Brainstorm setup for workshops

Updated: May 2023

Important notes

• Working with MEG/EEG recordings involves a lot of computational resources and large display windows. Therefore, we recommend that you bring a laptop with a decent processing capacity, at least 4GB RAM, a 64bit operating system, and a screen larger than 13".

• We strongly discourage the use of any Windows 32bit computer. The limitations of the memory management may result in "Out of memory" errors that will make difficult to follow the workshop content.

• You would add to your comfort by bringing an external mouse. Most of the manipulations are done with the mouse, and some involve an intensive use of the scrolling operation. A mouse wheel or the "two-finger move" on Apple MacBooks are perfect for this, but this operation is not always easy to perform on some laptops.

• Don't forget your power adapter!

• If the workshop indicates it, prepare a personal datasets that you would like to process with Brainstorm during the "analyze your data" section of the workshop.

Installing Brainstorm

Before coming to the workshop, you need to download Brainstorm (150 MB). To streamline troubleshooting during the session, please save all the downloaded files Desktop folder.

1. From the Brainstorm Download page, log in or create a Brainstorm account

2. Download Brainstorm in your Desktop folder:

   • Brainstorm software: brainstorm_YYMMDD.zip (150 MB)

     If you already have Brainstorm installed, make sure its version
     is not more than two months old.

3. Unzip the brainstorm_YYMMDD.zip file on your Desktop folder. Once done, delete the downloaded zip file.

4. Create a folder brainstorm_db on your Desktop

Final check: you should have now 2 folders on your Desktop:

1. brainstorm3: Program folder, with the source code and the compiled executable

2. brainstorm_db: Brainstorm database (empty)

Let's run Brainstorm, to make sure it works correctly on your computer (read the following section).

Running Brainstorm for the first time

With Matlab

• Matlab versions >= 2014b are faster and produce nicer graphics: consider upgrading if possible.

• Start Matlab

• Do NOT add the brainstorm3 folder to your Matlab path: this will be done automatically

• Go to the brainstorm3 folder

• Type brainstorm in the command window

• When asked for the Brainstorm database folder, pick the brainstorm_db you have just created on your Desktop

Without Matlab

1. Check that your operating system is supported by Matlab R2022b

2. Supported OSs for Windows, MacOS and Linux

   If your system is not listed here, try with these other versions: 2020b or 2015b

3. Download the Matlab Runtime R2022b (9.13) for your operating system: https://www.mathworks.com/products/compiler/matlab-runtime.html

4. Install the Matlab Runtime:

   Windows:

   1. Unzip the Matlab Runtime installer
   2. Double-click on the .exe and follow the instructions

   MacOS:

   1. Unzip the Matlab Runtime installer at the terminal using the unzip command

   2. At the terminal, type ./install

   Linux: From a terminal, unzip .zip, then run ./install

   1. Unzip the Matlab Runtime installer at the terminal using the unzip command

   2. At the terminal, type ./install

   If you are having trouble at installing the Matlab Runtime, consult this link: https://www.mathworks.com/help/compiler/install-the-matlab-runtime.html

5. To run Brainstorm, go to the folder brainstorm3/bin/R2022b/ and:

   Windows: Double-click on brainstorm3.bat

   MacOS: Double-click on brainstorm3.command and wait for instructions

   Linux: Open a terminal and run ./brainstorm3.command

6. If the startup process seems very long, try pressing ENTER after clicking on the terminal window.
7. On MacOS or Linux, you may be asked to select the folder where you installed the Matlab Runtime.

8. When asked for the Brainstorm database folder, pick the brainstorm_db you have just created on your Desktop.

Troubleshooting for Windows

• Your current user may not have the necessary privileges. If you are an administrator for your computer, you can do the following: right-click on brainstorm3.bat > Run as administrator.

• If you are not the administrator of your computer and Matlab or the Runtime are not installed in the standard paths, Brainstorm may have trouble finding them. To specify manually the path of the Runtime or Matlab folder, right-click on brainstorm3.bat > Edit. Fill the second line of the script (Example: @SET "MATLABROOT=C:\Program Files\MATLAB\MATLAB Runtime\R2022b"), save the file, and try to execute it again.

Troubleshooting for MacOS

• On recent versions of MacOS, you may get an error message "Application can't be opened because it is from an unidentified developer". This message would appear for all the programs that were not downloaded from the Apple app-store. To go around this verification: right-click on the application > Open, then click on the Open button.

• Other MacOS issues are discussed on the forum: Support for MacOS BigSur.

Troubleshooting for MacOS or Linux

• Some Linux Mint users have reported having interface issues, changing the graphical theme of their OS fixed this problem.

• From a terminal, make sure that the file brainstorm3.command is executable. Run the command chmod a+x brainstorm3.command

• If nothing happens, run:
  ./brainstorm3.command MATLABROOT
  With MATLABROOT being the Matlab Runtime 9.13 folder (ex: /Applications/MATLAB/Runtime/v913)

• Try with another binary release (you will need to install its corresponding Matlab Runtime). See at the bottom of the Download page

Make sure it works

In order to check if Brainstorm works properly or your computer, please follow these instructions:

• Create a new protocol: Menu File > New protocol.
  Set the name to "Test", don't change the other default options.

• In the folder "Default anatomy", double-click successively on the files: MRI, head, and cortex_15002V.
• It should open the figures below, make sure they work correctly:
  • Click in the MRI Viewer to move the slices
  • Click+move your mouse in the 3D figure to rotate it

  • Zoom in/out with the mouse wheel or the two-finger scroll on MacBook pads

  • The head surface should be transparent, with the brain visible through it

  

Troubleshooting

For any technical problem, please contact Raymundo Cassani ( raymundo.cassani@mcgill.ca )